Establishing environmental DNA and RNA protocols for the simultaneous detection of fish viruses from seawater
Abstract Aquatic viruses are major threats to global aquacultural productivity. While conventional diagnostic methods for disease investigation are laborious, time‐consuming, and often involve the sacrifice of animals, environmental DNA and RNA (eDNA/eRNA) tools have the potential in being non‐invas...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-01-01
|
| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.418 |
| _version_ | 1797277032905703424 |
|---|---|
| author | Yin Cheong Aden Ip Jing Chen Li Ying Tan Clara Lau Ying Hui Chan Ravendrakumar Shanmugavelu Balasubramaniam Wan Yen Jovinc Wong Kaitlyn Ng Zi Yan Brian Tan Charlene Judith Fernandez Siow Foong Chang Him Hoo Yap |
| author_facet | Yin Cheong Aden Ip Jing Chen Li Ying Tan Clara Lau Ying Hui Chan Ravendrakumar Shanmugavelu Balasubramaniam Wan Yen Jovinc Wong Kaitlyn Ng Zi Yan Brian Tan Charlene Judith Fernandez Siow Foong Chang Him Hoo Yap |
| author_sort | Yin Cheong Aden Ip |
| collection | DOAJ |
| description | Abstract Aquatic viruses are major threats to global aquacultural productivity. While conventional diagnostic methods for disease investigation are laborious, time‐consuming, and often involve the sacrifice of animals, environmental DNA and RNA (eDNA/eRNA) tools have the potential in being non‐invasive alternatives for the effective and early detection of various pathogens simultaneously. In this study, three seawater filtration methods—Sterivex syringe filtration, centrifugal ultrafiltration, and vacuum pump filtration with iron flocculation—were assessed for the recovery rates in co‐detecting fish virus eDNA/eRNA from natural seawater that was spiked with fish red seabream iridovirus (RSIV, DNA virus) and nervous necrosis virus (NNV, RNA virus). The centrifugal ultrafiltration method was the most effective for the capture of small‐sized viruses like NNV with a recovery rate of 63.23%, while the method of vacuum pump filtration with iron flocculation and chloroform disintegration of filter membranes had the highest RSIV recovery rate of 32.61%. We also optimized both automated and manual nucleic acid extraction methods and found comparable eDNA/eRNA extraction efficiencies. Our findings from the systematic comparison of seawater filtration and extraction methods suggest that each seawater filtration/nucleic acid extraction method can cater to different aquatic animal virus surveillance and disease investigation scenarios. These highlight the potential of virus eDNA/eRNA approaches for advancing the field of disease ecology and safeguarding aquatic animal health. |
| first_indexed | 2024-03-07T15:37:48Z |
| format | Article |
| id | doaj.art-98ff41e2783d44f6a67256258301929c |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-03-07T15:37:48Z |
| publishDate | 2024-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-98ff41e2783d44f6a67256258301929c2024-03-05T09:32:37ZengWileyEnvironmental DNA2637-49432024-01-0161n/an/a10.1002/edn3.418Establishing environmental DNA and RNA protocols for the simultaneous detection of fish viruses from seawaterYin Cheong Aden Ip0Jing Chen1Li Ying Tan2Clara Lau3Ying Hui Chan4Ravendrakumar Shanmugavelu Balasubramaniam5Wan Yen Jovinc Wong6Kaitlyn Ng7Zi Yan Brian Tan8Charlene Judith Fernandez9Siow Foong Chang10Him Hoo Yap11Animal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAnimal & Veterinary Service National Parks Board 1 Cluny Road Singapore City 259569 SingaporeAbstract Aquatic viruses are major threats to global aquacultural productivity. While conventional diagnostic methods for disease investigation are laborious, time‐consuming, and often involve the sacrifice of animals, environmental DNA and RNA (eDNA/eRNA) tools have the potential in being non‐invasive alternatives for the effective and early detection of various pathogens simultaneously. In this study, three seawater filtration methods—Sterivex syringe filtration, centrifugal ultrafiltration, and vacuum pump filtration with iron flocculation—were assessed for the recovery rates in co‐detecting fish virus eDNA/eRNA from natural seawater that was spiked with fish red seabream iridovirus (RSIV, DNA virus) and nervous necrosis virus (NNV, RNA virus). The centrifugal ultrafiltration method was the most effective for the capture of small‐sized viruses like NNV with a recovery rate of 63.23%, while the method of vacuum pump filtration with iron flocculation and chloroform disintegration of filter membranes had the highest RSIV recovery rate of 32.61%. We also optimized both automated and manual nucleic acid extraction methods and found comparable eDNA/eRNA extraction efficiencies. Our findings from the systematic comparison of seawater filtration and extraction methods suggest that each seawater filtration/nucleic acid extraction method can cater to different aquatic animal virus surveillance and disease investigation scenarios. These highlight the potential of virus eDNA/eRNA approaches for advancing the field of disease ecology and safeguarding aquatic animal health.https://doi.org/10.1002/edn3.418centrifugal ultrafiltrationeDNAeRNAiron flocculationnervous necrosis virus (NNV)red sea bream iridovirus (RSIV) |
| spellingShingle | Yin Cheong Aden Ip Jing Chen Li Ying Tan Clara Lau Ying Hui Chan Ravendrakumar Shanmugavelu Balasubramaniam Wan Yen Jovinc Wong Kaitlyn Ng Zi Yan Brian Tan Charlene Judith Fernandez Siow Foong Chang Him Hoo Yap Establishing environmental DNA and RNA protocols for the simultaneous detection of fish viruses from seawater Environmental DNA centrifugal ultrafiltration eDNA eRNA iron flocculation nervous necrosis virus (NNV) red sea bream iridovirus (RSIV) |
| title | Establishing environmental DNA and RNA protocols for the simultaneous detection of fish viruses from seawater |
| title_full | Establishing environmental DNA and RNA protocols for the simultaneous detection of fish viruses from seawater |
| title_fullStr | Establishing environmental DNA and RNA protocols for the simultaneous detection of fish viruses from seawater |
| title_full_unstemmed | Establishing environmental DNA and RNA protocols for the simultaneous detection of fish viruses from seawater |
| title_short | Establishing environmental DNA and RNA protocols for the simultaneous detection of fish viruses from seawater |
| title_sort | establishing environmental dna and rna protocols for the simultaneous detection of fish viruses from seawater |
| topic | centrifugal ultrafiltration eDNA eRNA iron flocculation nervous necrosis virus (NNV) red sea bream iridovirus (RSIV) |
| url | https://doi.org/10.1002/edn3.418 |
| work_keys_str_mv | AT yincheongadenip establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT jingchen establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT liyingtan establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT claralau establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT yinghuichan establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT ravendrakumarshanmugavelubalasubramaniam establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT wanyenjovincwong establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT kaitlynng establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT ziyanbriantan establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT charlenejudithfernandez establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT siowfoongchang establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater AT himhooyap establishingenvironmentaldnaandrnaprotocolsforthesimultaneousdetectionoffishvirusesfromseawater |